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2D2I
Asym. Unit
Info
Asym.Unit (341 KB)
Biol.Unit 1 (227 KB)
Biol.Unit 2 (222 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NADP-DEPENDENT GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM SYNECHOCOCCUS SP. COMPLEXED WITH NADP+
Authors
:
T. Kitatani, Y. Nakamura, K. Wada, T. Kinoshita, M. Tamoi, S. Shigeoka, T. Tada
Date
:
09 Sep 05 (Deposition) - 11 Jul 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,O,P,Q,R
Biol. Unit 1: A,B (2x)
Biol. Unit 2: O,P,Q,R (1x)
Keywords
:
Glyceraldehyde 3-Phosphate Dehydrogenase, Rossmann Fold, Protein-Nadp+ Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kitatani, Y. Nakamura, K. Wada, T. Kinoshita, M. Tamoi, S. Shigeoka, T. Tada
Structure Of Nadp-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase From Synechococcus Pcc7942 Complexed With Nadp
Acta Crystallogr. , Sect. F V. 62 315 2006
(for further references see the
PDB file header
)
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
1d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
1e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
1f: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAP
6
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:154 , THR A:213 , GLY A:214 , ALA A:215 , HOH A:6376 , HOH A:6410 , HOH A:6478 , HOH A:6805
BINDING SITE FOR RESIDUE SO4 A 1339
02
AC2
SOFTWARE
THR A:185 , ASP A:187 , ARG A:200 , ARG A:236 , NAP A:1341 , HOH A:6404 , HOH A:6417 , HOH A:6735 , HOH A:6782
BINDING SITE FOR RESIDUE SO4 A 1340
03
AC3
SOFTWARE
SER B:154 , THR B:213 , GLY B:214 , ALA B:215 , HOH B:6409 , HOH B:6711 , HOH B:6815 , HOH B:6825
BINDING SITE FOR RESIDUE SO4 B 2339
04
AC4
SOFTWARE
THR B:185 , ASP B:187 , ARG B:200 , ARG B:236 , NAP B:2341 , HOH B:6525 , HOH B:6731 , HOH B:6750 , HOH B:6804 , HOH B:6826
BINDING SITE FOR RESIDUE SO4 B 2340
05
AC5
SOFTWARE
SER O:154 , THR O:156 , THR O:213 , GLY O:214 , ALA O:215 , HOH O:6456 , HOH O:6838
BINDING SITE FOR RESIDUE SO4 O 3339
06
AC6
SOFTWARE
THR O:185 , ASP O:187 , ARG O:200 , ARG O:236 , NAP O:3341 , HOH O:6389
BINDING SITE FOR RESIDUE SO4 O 3340
07
AC7
SOFTWARE
SER P:154 , THR P:213 , GLY P:214 , ALA P:215 , HOH P:6600 , HOH P:6717
BINDING SITE FOR RESIDUE SO4 P 4339
08
AC8
SOFTWARE
THR P:185 , ASP P:187 , ARG P:200 , ARG P:236 , NAP P:4341 , HOH P:6395 , HOH P:6653
BINDING SITE FOR RESIDUE SO4 P 4340
09
AC9
SOFTWARE
SER Q:154 , THR Q:213 , GLY Q:214 , ALA Q:215 , HOH Q:6486
BINDING SITE FOR RESIDUE SO4 Q 5339
10
BC1
SOFTWARE
THR Q:185 , ASP Q:187 , ARG Q:200 , ARG Q:236 , NAP Q:5341 , HOH Q:6852
BINDING SITE FOR RESIDUE SO4 Q 5340
11
BC2
SOFTWARE
SER R:154 , THR R:213 , GLY R:214 , ALA R:215 , HOH R:6737 , HOH R:6832
BINDING SITE FOR RESIDUE SO4 R 6339
12
BC3
SOFTWARE
THR R:185 , ASP R:187 , ARG R:200 , ARG R:236 , NAP R:6341 , HOH R:6497 , HOH R:6858
BINDING SITE FOR RESIDUE SO4 R 6340
13
BC4
SOFTWARE
GLY A:9 , PHE A:10 , GLY A:11 , ARG A:12 , ILE A:13 , ASN A:35 , ASN A:36 , THR A:37 , ASP A:79 , ARG A:80 , SER A:98 , THR A:99 , GLY A:100 , VAL A:101 , THR A:122 , ALA A:123 , CYS A:155 , LEU A:186 , ASN A:318 , TYR A:322 , SO4 A:1340 , HOH A:6397 , HOH A:6417 , HOH A:6436 , HOH A:6513 , HOH A:6598 , HOH A:6797 , HOH A:6802 , SER B:194 , HOH B:6545 , HOH B:6599
BINDING SITE FOR RESIDUE NAP A 1341
14
BC5
SOFTWARE
SER A:194 , GLY B:9 , PHE B:10 , GLY B:11 , ARG B:12 , ILE B:13 , ASN B:36 , THR B:37 , ARG B:80 , SER B:98 , THR B:99 , GLY B:100 , THR B:122 , ALA B:123 , CYS B:155 , LEU B:186 , ASN B:318 , GLU B:319 , TYR B:322 , SO4 B:2340 , HOH B:6357 , HOH B:6440 , HOH B:6488 , HOH B:6536 , HOH B:6608 , HOH B:6613 , HOH B:6625 , HOH B:6804 , HOH B:6806
BINDING SITE FOR RESIDUE NAP B 2341
15
BC6
SOFTWARE
GLY O:9 , PHE O:10 , GLY O:11 , ARG O:12 , ILE O:13 , THR O:37 , ARG O:80 , SER O:98 , THR O:99 , GLY O:100 , THR O:122 , ALA O:123 , CYS O:155 , THR O:185 , LEU O:186 , ASN O:318 , TYR O:322 , SO4 O:3340 , HOH O:6515 , HOH O:6540 , HOH O:6562 , HOH O:6660 , HOH O:6719 , HOH O:6749 , HOH O:6836 , SER R:194 , HOH R:6833
BINDING SITE FOR RESIDUE NAP O 3341
16
BC7
SOFTWARE
GLY P:9 , PHE P:10 , GLY P:11 , ARG P:12 , ILE P:13 , ASN P:35 , THR P:37 , ARG P:80 , SER P:98 , THR P:99 , GLY P:100 , THR P:122 , ALA P:123 , CYS P:155 , LEU P:186 , ASN P:318 , GLU P:319 , TYR P:322 , SO4 P:4340 , HOH P:6395 , HOH P:6578 , HOH P:6638 , HOH P:6653 , HOH P:6664 , HOH P:6876 , SER Q:194 , HOH Q:6709
BINDING SITE FOR RESIDUE NAP P 4341
17
BC8
SOFTWARE
SER P:194 , HOH P:6659 , GLY Q:9 , PHE Q:10 , GLY Q:11 , ARG Q:12 , ILE Q:13 , ASN Q:35 , THR Q:37 , ARG Q:80 , SER Q:98 , THR Q:99 , GLY Q:100 , THR Q:122 , ALA Q:123 , CYS Q:155 , LEU Q:186 , ASN Q:318 , GLU Q:319 , TYR Q:322 , SO4 Q:5340 , HOH Q:6457 , HOH Q:6470 , HOH Q:6552 , HOH Q:6752
BINDING SITE FOR RESIDUE NAP Q 5341
18
BC9
SOFTWARE
SER O:194 , GLY R:9 , GLY R:11 , ARG R:12 , ILE R:13 , ASN R:35 , THR R:37 , ARG R:80 , SER R:98 , THR R:99 , GLY R:100 , VAL R:101 , PHE R:102 , THR R:122 , ALA R:123 , CYS R:155 , LEU R:186 , ASN R:318 , GLU R:319 , TYR R:322 , SO4 R:6340 , HOH R:6637 , HOH R:6846
BINDING SITE FOR RESIDUE NAP R 6341
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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;
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2d2iA02 (A:154-318)
1b: CATH_2d2iB02 (B:154-318)
1c: CATH_2d2iO02 (O:154-318)
1d: CATH_2d2iP02 (P:154-318)
1e: CATH_2d2iQ02 (Q:154-318)
1f: CATH_2d2iR02 (R:154-318)
2a: CATH_2d2iA01 (A:1-153,A:319-338)
2b: CATH_2d2iB01 (B:1-153,B:319-338)
2c: CATH_2d2iO01 (O:1-153,O:319-338)
2d: CATH_2d2iP01 (P:1-153,P:319-338)
2e: CATH_2d2iQ01 (Q:1-153,Q:319-338)
2f: CATH_2d2iR01 (R:1-153,R:319-338)
View:
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Classes
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(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Synechococcus sp.. Organism_taxid: 1131.
(1)
1a
2d2iA02
A:154-318
1b
2d2iB02
B:154-318
1c
2d2iO02
O:154-318
1d
2d2iP02
P:154-318
1e
2d2iQ02
Q:154-318
1f
2d2iR02
R:154-318
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Synechococcus sp.. Organism_taxid: 1131.
(1)
2a
2d2iA01
A:1-153,A:319-338
2b
2d2iB01
B:1-153,B:319-338
2c
2d2iO01
O:1-153,O:319-338
2d
2d2iP01
P:1-153,P:319-338
2e
2d2iQ01
Q:1-153,Q:319-338
2f
2d2iR01
R:1-153,R:319-338
[
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]
Pfam Domains
(0, 0)
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Asym.Unit (341 KB)
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